Dear list,
  I am confused with my problem and hope get some help from you.
  I have 5 groups of sample, each with 3 samples (all AFFY).  I first read in all the 15 samples and did lmFit.  I am interested in the difference between group1 and group2, so I made a contrast matrix with "group1-group2".  Then I only read the 6 samples of group1 and group2 and did the same thing.  However, the differentially expressed gene list are very different.
  I used gcrma to normalize the dataset.  Do you think the difference is caused by normalization or I did something wrong?
  Thanks,
  Lisa

		
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